When using MACS2 with -f BAM, it is possible to have a shift other than 0?
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3.1 years ago
Lucy ▴ 80

Hi,

In the manual for MACS2, there is the following statement in the information about the --shift option: "Note, you can't set values other than 0 if format is BAMPE or BEDPE for paired-end data. Default is 0"

Is this also the case if the format is set as BAM or can I have different shift sizes with BAM? The command I would like to use to analyse my ATAC-seq data is as follows:

macs2 callpeak <input file> -f BAM --no-model --shift -100 --extsize 200 --keep-dup-all --call-summits


Many thanks, Lucy

macs2 macs • 895 views
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My understanding is that you do not need any shifting parameters when using --nomodel. Is this ATAC-seq?

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Yes this is ATAC-seq data.

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Did you solve your problem or do you need further assistance? You raised this question in different posts, that is why I am asking.

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Thanks for the message. I think I have decided to go with -f BAMPE and no shifting.